Protein Structure Modeling with MODELLER

Benjamin Webb; Andrej Sali

doi:10.1007/978-1-0716-0892-0_14

Protein Structure Modeling with MODELLER

Methods Mol Biol. 2021:2199:239-255. doi: 10.1007/978-1-0716-0892-0_14.

Authors

Benjamin Webb^{1

2

3}, Andrej Sali^{4

5

6}

Affiliations

¹ Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
² Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
³ California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, USA.
⁴ Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. sali@salilab.org.
⁵ Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. sali@salilab.org.
⁶ California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, USA. sali@salilab.org.

PMID: 33125654
DOI: 10.1007/978-1-0716-0892-0_14

Abstract

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

Keywords: Comparative modeling; Fold assignment; Model assessment; Multiple templates; Sequence-structure alignment.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Databases, Protein*
Models, Molecular*
Protein Conformation
Proteins / chemistry*
Software*

Substances

Proteins

Grants and funding

U54 GM094625/GM/NIGMS NIH HHS/United States